1
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Hoenger Ramazanova RD, Roumeliotis TI, Wright JC, Choudhary JS. PhoXplex: Combining Phospho-enrichable Cross-Linking with Isobaric Labeling for Quantitative Proteome-Wide Mapping of Protein Interfaces. J Proteome Res 2024. [PMID: 39422127 DOI: 10.1021/acs.jproteome.4c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Integrating cross-linking mass spectrometry (XL-MS) into structural biology workflows provides valuable information about the spatial arrangement of amino acid stretches, which can guide elucidation of protein assembly architecture. Additionally, the combination of XL-MS with peptide quantitation techniques is a powerful approach to delineate protein interface dynamics across diverse conditions. While XL-MS is increasingly effective with isolated proteins or small complexes, its application to whole-cell samples poses technical challenges related to analysis depth and throughput. The use of enrichable cross-linkers has greatly improved the detectability of protein interfaces in a proteome-wide scale, facilitating global protein-protein interaction mapping. Therefore, bringing together enrichable cross-linking and multiplexed peptide quantification is an appealing approach to enable comparative characterization of structural attributes of proteins and protein interactions. Here, we combined phospho-enrichable cross-linking with TMT labeling to develop a streamline workflow (PhoXplex) for the detection of differential structural features across a panel of cell lines in a global scale. We achieved deep coverage with quantification of over 9000 cross-links and long loop-links in total including potentially novel interactions. Overlaying AlphaFold predictions and disorder protein annotations enables exploration of the quantitative cross-linking data set, to reveal possible associations between mutations and protein structures. Lastly, we discuss current shortcomings and perspectives for deep whole-cell profiling of protein interfaces at large-scale.
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Affiliation(s)
- Runa D Hoenger Ramazanova
- Functional Proteomics team, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Theodoros I Roumeliotis
- Functional Proteomics team, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - James C Wright
- Functional Proteomics team, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Jyoti S Choudhary
- Functional Proteomics team, Chester Beatty Laboratories, The Institute of Cancer Research, London SW3 6JB, United Kingdom
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2
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Zhao L, An Y, Zhao N, Gao H, Zhang W, Gong Z, Liu X, Zhao B, Liang Z, Tang C, Zhang L, Zhang Y, Zhao Q. Spatially resolved profiling of protein conformation and interactions by biocompatible chemical cross-linking in living cells. Nat Commun 2024; 15:8331. [PMID: 39333085 PMCID: PMC11436894 DOI: 10.1038/s41467-024-52558-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/12/2024] [Indexed: 09/29/2024] Open
Abstract
Unlocking the intricacies of protein structures and interactions within the dynamic landscape of subcellular organelles presents a significant challenge. To address this, we introduce SPACX, a method for spatially resolved protein complex profiling via biocompatible chemical cross(x)-linking with subcellular isolation, designed to monitor protein conformation, interactions, and translocation in living cells. By rapidly capturing protein complexes in their native physiological state and efficiently enriching cross-linked peptides, SPACX allows comprehensive analysis of the protein interactome within living cells. Leveraging structure refinement with cross-linking restraints, we identify subcellular-specific conformation heterogeneity of PTEN, revealing dynamic differences in its dual specificity domains between the nucleus and cytoplasm. Furthermore, by discerning conformational disparities, we identify 83 cytoplasm-exclusive and 109 nucleus-exclusive PTEN-interacting proteins, each associated with distinct biological functions. Upon induction of ubiquitin-proteasome system stress, we observe dynamic alterations in PTEN assembly and its interacting partners during translocation. These changes, including the identification of components and interaction sites, are characterized using the SPACX approach. Notably, SPACX enables identification of unique interacting proteins specific to PTEN isoforms, including PTEN and PTEN-Long, through the determination of sequence-specific cross-linking interfaces. These findings underscore the potential of SPACX to elucidate the functional diversity of proteins within distinct subcellular sociology.
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Affiliation(s)
- Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin An
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Nan Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weijie Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhou Gong
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaolong Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Chun Tang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Beijing, China
- Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China.
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3
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Combe CW, Graham M, Kolbowski L, Fischer L, Rappsilber J. xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data. J Mol Biol 2024; 436:168656. [PMID: 39237202 DOI: 10.1016/j.jmb.2024.168656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/17/2024] [Accepted: 06/07/2024] [Indexed: 09/07/2024]
Abstract
Crosslinking mass spectrometry (MS) has emerged as an important technique for elucidating the in-solution structures of protein complexes and the topology of protein-protein interaction networks. However, the expanding user community lacked an integrated visualisation tool that helped them make use of the crosslinking data for investigating biological mechanisms. We addressed this need by developing xiVIEW, a web-based application designed to streamline crosslinking MS data analysis, which we present here. xiVIEW provides a user-friendly interface for accessing coordinated views of mass spectrometric data, network visualisation, annotations extracted from trusted repositories like UniProtKB, and available 3D structures. In accordance with recent recommendations from the crosslinking MS community, xiVIEW (i) provides a standards compliant parser to improve data integration and (ii) offers accessible visualisation tools. By promoting the adoption of standard file formats and providing a comprehensive visualisation platform, xiVIEW empowers both experimentalists and modellers alike to pursue their respective research interests. We anticipate that xiVIEW will advance crosslinking MS-inspired research, and facilitate broader and more effective investigations into complex biological systems.
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Affiliation(s)
- Colin W Combe
- University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JR, UK.
| | - Martin Graham
- University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JR, UK
| | - Lars Kolbowski
- University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JR, UK; Technische Universität Berlin, 10623 Berlin, Germany
| | - Lutz Fischer
- Technische Universität Berlin, 10623 Berlin, Germany.
| | - Juri Rappsilber
- University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JR, UK; Technische Universität Berlin, 10623 Berlin, Germany.
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4
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Lacey SE, Graziadei A, Pigino G. Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport. Cell 2024; 187:4621-4636.e18. [PMID: 39067443 PMCID: PMC11349379 DOI: 10.1016/j.cell.2024.06.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/06/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell to the cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.
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5
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Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BJM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med 2024:S1471-4914(24)00195-3. [PMID: 39152082 DOI: 10.1016/j.molmed.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yu Mi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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6
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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024; 124:9113-9135. [PMID: 39008623 PMCID: PMC11327963 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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7
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Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L. Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606913. [PMID: 39211111 PMCID: PMC11360931 DOI: 10.1101/2024.08.06.606913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric cross-links can offer enhanced spatial resolution to facilitate the characterization of dynamic and heterogeneous protein complexes. However, the identification of multimeric cross-links remains extremely challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MS n analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks. The trimeric interactions captured by TSTO have uncovered new structural details that cannot be easily revealed by existing reagents, allowing in-depth description of PPIs to facilitate structural modeling. This development not only advances XL-MS technologies for global PPI profiling from living cells, but also offers a new direction for creating multifunctional MS-cleavable cross-linkers to further push structural systems biology forward in the future.
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8
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Jiao F, Yu C, Wheat A, Chen L, Lih TSM, Zhang H, Huang L. DSBSO-Based XL-MS Analysis of Breast Cancer PDX Tissues to Delineate Protein Interaction Network in Clinical Samples. J Proteome Res 2024; 23:3269-3279. [PMID: 38334954 PMCID: PMC11296914 DOI: 10.1021/acs.jproteome.3c00832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Protein-protein interactions (PPIs) are fundamental to understanding biological systems as protein complexes are the active molecular modules critical for carrying out cellular functions. Dysfunctional PPIs have been associated with various diseases including cancer. Systems-wide PPI analysis not only sheds light on pathological mechanisms, but also represents a paradigm in identifying potential therapeutic targets. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for defining endogenous PPIs of cellular networks. While proteome-wide studies have been performed in cell lysates, intact cells and tissues, applications of XL-MS in clinical samples have not been reported. In this study, we adopted a DSBSO-based in vivo XL-MS platform to map interaction landscapes from two breast cancer patient-derived xenograft (PDX) models. As a result, we have generated a PDX interaction network comprising 2,557 human proteins and identified interactions unique to breast cancer subtypes. Interestingly, most of the observed differences in PPIs correlated well with protein abundance changes determined by TMT-based proteome quantitation. Collectively, this work has demonstrated the feasibility of XL-MS analysis in clinical samples, and established an analytical workflow for tissue cross-linking that can be generalized for mapping PPIs from patient samples in the future to dissect disease-relevant cellular networks.
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Affiliation(s)
- Fenglong Jiao
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Andrew Wheat
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| | - Lijun Chen
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Tung-Shing Mamie Lih
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Hui Zhang
- Department of Pathology and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
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9
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Kadavá T, Hevler JF, Kalaidopoulou Nteak S, Yin VC, Strasser J, Preiner J, Heck AJ. Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum. EMBO J 2024; 43:3009-3026. [PMID: 38811852 PMCID: PMC11251186 DOI: 10.1038/s44318-024-00128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024] Open
Abstract
The complement is a conserved cascade that plays a central role in the innate immune system. To maintain a delicate equilibrium preventing excessive complement activation, complement inhibitors are essential. One of the major fluid-phase complement inhibitors is C4b-binding protein (C4BP). Human C4BP is a macromolecular glycoprotein composed of two distinct subunits, C4BPα and C4BPβ. These associate with vitamin K-dependent protein S (ProS) forming an ensemble of co-occurring higher-order structures. Here, we characterize these C4BP assemblies. We resolve and quantify isoforms of purified human serum C4BP using distinct single-particle detection techniques: charge detection mass spectrometry, and mass photometry accompanied by high-speed atomic force microscopy. Combining cross-linking mass spectrometry, glycoproteomics, and structural modeling, we report comprehensive glycoproteoform profiles and full-length structural models of the endogenous C4BP assemblies, expanding knowledge of this key complement inhibitor's structure and composition. Finally, we reveal that an increased C4BPα to C4BPβ ratio coincides with elevated C-reactive protein levels in patient plasma samples. This observation highlights C4BP isoform variation and affirms a distinct role of co-occurring C4BP assemblies upon acute phase inflammation.
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Affiliation(s)
- Tereza Kadavá
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Sofia Kalaidopoulou Nteak
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Victor C Yin
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Juergen Strasser
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020, Linz, Austria
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
- Netherlands Proteomics Center, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
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10
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Modic M, Adamek M, Ule J. The impact of IDR phosphorylation on the RNA binding profiles of proteins. Trends Genet 2024; 40:580-586. [PMID: 38705823 DOI: 10.1016/j.tig.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to their capacity to mediate repetitive protein interactions, intrinsically disordered regions (IDRs) are crucial for the formation of various types of protein-RNA complexes. The functions of IDRs are strongly modulated by post-translational modifications (PTMs). Phosphorylation is the most common and well-studied modification of IDRs, which can alter homomeric or heteromeric interactions of proteins and impact their ability to phase separate. Moreover, phosphorylation can influence the RNA-binding properties of proteins, and recent studies demonstrated its selective impact on the global profiles of protein-RNA binding and regulation. These findings highlight the need for further integrative approaches to understand how signalling remodels protein-RNA networks in cells.
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Affiliation(s)
- Miha Modic
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
| | - Maksimiljan Adamek
- National Institute of Chemistry, Ljubljana, Slovenia; PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Ljubljana, Slovenia; The Francis Crick Institute, London, UK; UK Dementia Research Institute at King's College London, London, UK.
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11
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Akkulak H, İnce HK, Goc G, Lebrilla CB, Kabasakal BV, Ozcan S. Structural proteomics of a bacterial mega membrane protein complex: FtsH-HflK-HflC. Int J Biol Macromol 2024; 269:131923. [PMID: 38697437 DOI: 10.1016/j.ijbiomac.2024.131923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Recent advances in mass spectrometry (MS) yielding sensitive and accurate measurements along with developments in software tools have enabled the characterization of complex systems routinely. Thus, structural proteomics and cross-linking mass spectrometry (XL-MS) have become a useful method for structural modeling of protein complexes. Here, we utilized commonly used XL-MS software tools to elucidate the protein interactions within a membrane protein complex containing FtsH, HflK, and HflC, over-expressed in E. coli. The MS data were processed using MaxLynx, MeroX, MS Annika, xiSEARCH, and XlinkX software tools. The number of identified inter- and intra-protein cross-links varied among software. Each interaction was manually checked using the raw MS and MS/MS data and distance restraints to verify inter- and intra-protein cross-links. A total of 37 inter-protein and 148 intra-protein cross-links were determined in the FtsH-HflK-HflC complex. The 59 of them were new interactions on the lacking region of recently published structures. These newly identified interactions, when combined with molecular docking and structural modeling, present opportunities for further investigation. The results provide valuable information regarding the complex structure and function to decipher the intricate molecular mechanisms underlying the FtsH-HflK-HflC complex.
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Affiliation(s)
- Hatice Akkulak
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye
| | - H Kerim İnce
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye
| | - Gunce Goc
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara 06830, Turkiye
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, 95616, CA, USA
| | - Burak V Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara 06830, Turkiye; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Sureyya Ozcan
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkiye; Cancer Systems Biology Laboratory (CanSyL), Middle East Technical University, 06800 Ankara, Turkiye
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12
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Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem 2024; 96:7373-7379. [PMID: 38696819 PMCID: PMC11099889 DOI: 10.1021/acs.analchem.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.
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Affiliation(s)
- Juan Camilo Rojas Echeverri
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Frank Hause
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Institute
for Molecular Medicine, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Claudio Iacobucci
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Department
of Physical and Chemical Sciences, University
of L’Aquila, 67100 L’Aquila, Italy
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Dirk Tänzler
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
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13
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Chen T, Chen Z, Wu P, Luo J, Liu Q, Yang H, Peng C, Zhang G, Lin H, Ji Z. The Interaction between ADK and SCG10 Regulate the Repair of Nerve Damage. Neuroscience 2024; 544:75-87. [PMID: 38423163 DOI: 10.1016/j.neuroscience.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024]
Abstract
The cytoskeleton must be remodeled during neurite outgrowth, and Superior Cervical Ganglion 10 (SCG10) plays a critical role in this process by depolymerizing Microtubules (MTs), conferring highly dynamic properties to the MTs. However, the precise mechanism of action of SCG10 in the repair of injured neurons remains largely uncertain. Using transcriptomic identification, we discovered that SCG10 expression was downregulated in neurons after Spinal Cord Injury (SCI). Additionally, through mass spectrometry identification, immunoprecipitation, and pull-down assays, we established that SCG10 could interact with Adenosine Kinase (ADK). Furthermore, we developed an excitotoxicity-induced neural injury model and discovered that ADK suppressed injured neurite re-growth, whereas, through overexpression and small molecule interference experiments, SCG10 enhanced it. Moreover, we discovered ADK to be the upstream of SCG10. More importantly, the application of the ADK inhibitor called 5-Iodotubercidin (5-ITu) was found to significantly enhance the recovery of motor function in mice with SCI. Consequently, our findings suggest that ADK plays a negative regulatory role in the repair of injured neurons. Herein, we propose a molecular interaction model of the SCG10-ADK axis to regulate neuronal recovery.
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Affiliation(s)
- Tianjun Chen
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Zhiwan Chen
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Ping Wu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Jianxian Luo
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Qiuling Liu
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Hua Yang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Cheng Peng
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Guowei Zhang
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Hongsheng Lin
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China
| | - Zhisheng Ji
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangdong Province, Guangzhou 510630, People's Republic of China.
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14
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 PMCID: PMC11211576 DOI: 10.1038/s41586-024-07198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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15
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Di Ianni A, Di Ianni A, Cowan K, Barbero LM, Sirtori FR. Leveraging Cross-Linking Mass Spectrometry for Modeling Antibody-Antigen Complexes. J Proteome Res 2024; 23:1049-1061. [PMID: 38372774 DOI: 10.1021/acs.jproteome.3c00816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Elucidating antibody-antigen complexes at the atomic level is of utmost interest for understanding immune responses and designing better therapies. Cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for mapping protein-protein interactions, suggesting valuable structural insights. However, the use of XL-MS studies to enable epitope/paratope mapping of antibody-antigen complexes is still limited up to now. XL-MS data can be used to drive integrative modeling of antibody-antigen complexes, where cross-links information serves as distance restraints for the precise determination of binding interfaces. In this approach, XL-MS data are employed to identify connections between binding interfaces of the antibody and the antigen, thus informing molecular modeling. Current literature provides minimal input about the impact of XL-MS data on the integrative modeling of antibody-antigen complexes. Here, we applied XL-MS to retrieve information about binding interfaces of three antibody-antigen complexes. We leveraged XL-MS data to perform integrative modeling using HADDOCK (active-passive residues and distance restraints strategies) and AlphaLink2. We then compared these three approaches with initial predictions of investigated antibody-antigen complexes by AlphaFold Multimer. This work emphasizes the importance of cross-linking data in resolving conformational dynamics of antibody-antigen complexes, ultimately enhancing the design of better protein therapeutics and vaccines.
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Affiliation(s)
- Andrea Di Ianni
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
- University of Turin, Molecular Biotechnology Center, Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Alessio Di Ianni
- Martin Luther University Halle-Wittenberg, Department of Pharmaceutical Chemistry and Bioanalytics, Center for Structural Mass Spectrometry, Institute of Pharmacy, Kurt-Mothes-Str. 3, Halle/Saale D-06120, Germany
| | - Kyra Cowan
- New Biological Entities, Drug Metabolism and Pharmacokinetics (NBE-DMPK), Research and Development, Merck KGaA, Frankfurterstrasse 250, Darmstadt 64293, Germany
| | - Luca M Barbero
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
| | - Federico Riccardi Sirtori
- NBE-DMPK Innovative BioAnalytics, Merck Serono RBM S.p.A., an Affiliate of Merck KGaA, Darmstadt, Germany, Via Ribes 1, Colleretto Giacosa (TO) 10010, Italy
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16
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Garrison AR, Moresco V, Zeng X, Cline CR, Ward MD, Ricks KM, Olschner SP, Cazares LH, Karaaslan E, Fitzpatrick CJ, Bergeron É, Pegan SD, Golden JW. Nucleocapsid protein-specific monoclonal antibodies protect mice against Crimean-Congo hemorrhagic fever virus. Nat Commun 2024; 15:1722. [PMID: 38409240 PMCID: PMC10897337 DOI: 10.1038/s41467-024-46110-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a WHO priority pathogen. Antibody-based medical countermeasures offer an important strategy to mitigate severe disease caused by CCHFV. Most efforts have focused on targeting the viral glycoproteins. However, glycoproteins are poorly conserved among viral strains. The CCHFV nucleocapsid protein (NP) is highly conserved between CCHFV strains. Here, we investigate the protective efficacy of a CCHFV monoclonal antibody targeting the NP. We find that an anti-NP monoclonal antibody (mAb-9D5) protected female mice against lethal CCHFV infection or resulted in a significant delay in mean time-to-death in mice that succumbed to disease compared to isotype control animals. Antibody protection is independent of Fc-receptor functionality and complement activity. The antibody bound NP from several CCHFV strains and exhibited robust cross-protection against the heterologous CCHFV strain Afg09-2990. Our work demonstrates that the NP is a viable target for antibody-based therapeutics, providing another direction for developing immunotherapeutics against CCHFV.
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Affiliation(s)
- Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA.
| | - Vanessa Moresco
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Curtis R Cline
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Michael D Ward
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Keersten M Ricks
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Scott P Olschner
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Lisa H Cazares
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Elif Karaaslan
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Collin J Fitzpatrick
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Scott D Pegan
- Division of Biomedical Sciences, University of California Riverside, Riverside, CA, USA
- Department of Chemistry & Life Science, United States Military Academy, West Point, NY, USA
| | - Joseph W Golden
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA.
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17
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Zhang Z, Zhao Q, Gong Z, Du R, Liu M, Zhang Y, Zhang L, Li C. Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology. JACS AU 2024; 4:369-383. [PMID: 38425916 PMCID: PMC10900494 DOI: 10.1021/jacsau.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024]
Abstract
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, understanding the changes in protein structures and interactions in response to stimuli within living cells, under both normal and disease conditions, is key to grasping proteins' functionality and cellular processes. Nevertheless, achieving high-resolution identification of these protein structures and interactions within living cells presents a technical challenge. In this Perspective, we summarize the recent advancements in in-cell nuclear magnetic resonance (NMR) and in vivo cross-linking mass spectrometry (XL-MS) for studying protein structures and interactions within a cellular context. Additionally, we discuss the challenges, opportunities, and potential benefits of integrating in-cell NMR and in vivo XL-MS in future research to offer an exhaustive approach to studying proteins in their natural habitat.
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Affiliation(s)
- Zeting Zhang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Zhao
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Zhou Gong
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ruichen Du
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- University
of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yukui Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Lihua Zhang
- CAS
Key Laboratory of Separation Science for Analytical Chemistry, National
Chromatographic R. & A. Center, State Key Laboratory of Medical
Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
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18
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Nouchikian L, Fernandez-Martinez D, Renard PY, Sabot C, Duménil G, Rey M, Chamot-Rooke J. Do Not Waste Time─Ensure Success in Your Cross-Linking Mass Spectrometry Experiments before You Begin. Anal Chem 2024; 96:2506-2513. [PMID: 38294351 PMCID: PMC10867798 DOI: 10.1021/acs.analchem.3c04682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has become a very useful tool for studying protein complexes and interactions in living systems. It enables the investigation of many large and dynamic assemblies in their native state, providing an unbiased view of their protein interactions and restraints for integrative modeling. More researchers are turning toward trying XL-MS to probe their complexes of interest, especially in their native environments. However, due to the presence of other potentially higher abundant proteins, sufficient cross-links on a system of interest may not be reached to achieve satisfactory structural and interaction information. There are currently no rules for predicting whether XL-MS experiments are likely to work or not; in other words, if a protein complex of interest will lead to useful XL-MS data. Here, we show that a simple iBAQ (intensity-based absolute quantification) analysis performed from trypsin digest data can provide a good understanding of whether proteins of interest are abundant enough to achieve successful cross-linking data. Comparing our findings to large-scale data on diverse systems from several other groups, we show that proteins of interest should be at least in the top 20% abundance range to expect more than one cross-link found per protein. We foresee that this guideline is a good starting point for researchers who would like to use XL-MS to study their protein of interest and help ensure a successful cross-linking experiment from the beginning. Data are available via ProteomeXchange with identifier PXD045792.
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Affiliation(s)
- Lucienne Nouchikian
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - David Fernandez-Martinez
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Pierre-Yves Renard
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Cyrille Sabot
- Univ
Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA
UMR 6014, INC3M FR 3038, Rouen F-76000, France
| | - Guillaume Duménil
- Institut
Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis
of Vascular Infections Unit, Paris 75015, France
| | - Martial Rey
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
| | - Julia Chamot-Rooke
- Institut
Pasteur, Université Paris Cité, CNRS UAR 2024, Mass
Spectrometry for Biology Unit, Paris 75015, France
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19
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Selcuk K, Leitner A, Braun L, Le Blanc F, Pacak P, Pot S, Vogel V. Transglutaminase 2 has higher affinity for relaxed than for stretched fibronectin fibers. Matrix Biol 2024; 125:113-132. [PMID: 38135164 DOI: 10.1016/j.matbio.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
Transglutaminase 2 (TG2) plays a vital role in stabilizing extracellular matrix (ECM) proteins through enzymatic crosslinking during tissue growth, repair, and inflammation. TG2 also binds non-covalently to fibronectin (FN), an essential component of the ECM, facilitating cell adhesion, migration, proliferation, and survival. However, the interaction between TG2 and fibrillar FN remains poorly understood, as most studies have focused on soluble or surface-adsorbed FN or FN fragments, which differ in their conformations from insoluble FN fibers. Using a well-established in vitro FN fiber stretch assay, we discovered that the binding of a crosslinking enzyme to ECM fibers is mechano-regulated. TG2 binding to FN is tuned by the mechanical tension of FN fibers, whereby TG2 predominantly co-localizes to low-tension FN fibers, while fiber stretching reduces their affinity for TG2. This mechano-regulated binding relies on the proximity between the N-terminal β-sandwich and C-terminal β-barrels of TG2. Crosslinking mass spectrometry (XL-MS) revealed a novel TG2-FN synergy site within TG2's C-terminal β-barrels that interacts with FN regions located outside of the canonical gelatin binding domain, specifically FNI2 and FNIII14-15. Combining XL-MS distance restraints with molecular docking revealed the mechano-regulated binding mechanism between TG2 and modules FNI7-9 by which mechanical forces regulate TG2-FN interactions. This highlights a previously unrecognized role of TG2 as a tension sensor for FN fibers. This novel interaction mechanism has significant implications in physiology and mechanobiology, including how forces regulate cell adhesion, spreading, migration, phenotype modulation, depending on the tensional state of ECM fibers. Data are available via ProteomeXchange with identifier PXD043976.
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Affiliation(s)
- Kateryna Selcuk
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Lukas Braun
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Fanny Le Blanc
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - Paulina Pacak
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Simon Pot
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland
| | - Viola Vogel
- Department of Health Sciences and Technology, Institute of Translational Medicine, Laboratory of Applied Mechanobiology, ETH Zurich, Gloriastrasse 37-39 GLC G11, CH-8092 Zurich, Switzerland.
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20
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Ozden B, Kryshtafovych A, Karaca E. The impact of AI-based modeling on the accuracy of protein assembly prediction: Insights from CASP15. Proteins 2023; 91:1636-1657. [PMID: 37861057 PMCID: PMC10873090 DOI: 10.1002/prot.26598] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023]
Abstract
In CASP15, 87 predictors submitted around 11 000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact predictions, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases, the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas, and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes also remains challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved a 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, USA
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
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21
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Stahl K, Graziadei A, Dau T, Brock O, Rappsilber J. Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning. Nat Biotechnol 2023; 41:1810-1819. [PMID: 36941363 PMCID: PMC10713450 DOI: 10.1038/s41587-023-01704-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its network architecture. By employing sparse experimental contacts as anchor points, AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets. We confirm this experimentally by using the noncanonical amino acid photo-leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. The program can predict distinct conformations of proteins on the basis of the distance restraints provided, demonstrating the value of experimental data in driving protein structure prediction. The noise-tolerant framework for integrating data in protein structure prediction presented here opens a path to accurate characterization of protein structures from in-cell data.
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Affiliation(s)
- Kolja Stahl
- Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, Germany
| | - Andrea Graziadei
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Therese Dau
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
- Fritz Lipmann Institute, Leibniz Institute on Aging, Jena, Germany
| | - Oliver Brock
- Robotics and Biology Laboratory, Technische Universität Berlin, Berlin, Germany.
- Science of Intelligence, Research Cluster of Excellence, Berlin, Germany.
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany.
- Si-M/'Der Simulierte Mensch', a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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22
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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23
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Ruwolt M, Piazza I, Liu F. The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol 2023; 82:102648. [PMID: 37423038 DOI: 10.1016/j.sbi.2023.102648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on endogenous protein-protein interaction (PPI) networks and protein binding interfaces. These features make XL-MS an attractive tool to support the development of PPI-targeting drugs. Though not yet widely used, applications of XL-MS to drug characterization are beginning to emerge. Here, we compare XL-MS to established structural proteomics methods in drug research, discuss the current state and remaining challenges of XL-MS technology, and provide a perspective on the future role XL-MS can play in drug development, with a particular emphasis on PPI modulators.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany. https://twitter.com/@MRuwolt
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany.
| | - Fan Liu
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany.
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24
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Yu C, Huang L. New advances in cross-linking mass spectrometry toward structural systems biology. Curr Opin Chem Biol 2023; 76:102357. [PMID: 37406423 PMCID: PMC11091472 DOI: 10.1016/j.cbpa.2023.102357] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023]
Abstract
Elucidating protein-protein interaction (PPI) networks and their structural features within cells is central to understanding fundamental biology and associations of cell phenotypes with human pathologies. Owing to technological advancements during the last decade, cross-linking mass spectrometry (XL-MS) has become an enabling technology for delineating interaction landscapes of proteomes as they exist in living systems. XL-MS is unique due to its capability to simultaneously capture PPIs from native environments and uncover interaction contacts though identification of cross-linked peptides, thereby permitting the determination of both identity and connectivity of PPIs in cells. In combination with high resolution structural tools such as cryo-electron microscopy and AI-assisted prediction, XL-MS has contributed significantly to elucidating architectures of large protein assemblies. This review highlights the latest developments in XL-MS technologies and their applications in proteome-wide analysis to advance structural systems biology.
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Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
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25
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Ozden B, Kryshtafovych A, Karaca E. The Impact of AI-Based Modeling on the Accuracy of Protein Assembly Prediction: Insights from CASP15. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548341. [PMID: 37503072 PMCID: PMC10369898 DOI: 10.1101/2023.07.10.548341] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
In CASP15, 87 predictors submitted around 11,000 models on 41 assembly targets. The community demonstrated exceptional performance in overall fold and interface contact prediction, achieving an impressive success rate of 90% (compared to 31% in CASP14). This remarkable accomplishment is largely due to the incorporation of DeepMind's AF2-Multimer approach into custom-built prediction pipelines. To evaluate the added value of participating methods, we compared the community models to the baseline AF2-Multimer predictor. In over 1/3 of cases the community models were superior to the baseline predictor. The main reasons for this improved performance were the use of custom-built multiple sequence alignments, optimized AF2-Multimer sampling, and the manual assembly of AF2-Multimer-built subcomplexes. The best three groups, in order, are Zheng, Venclovas and Wallner. Zheng and Venclovas reached a 73.2% success rate over all (41) cases, while Wallner attained 69.4% success rate over 36 cases. Nonetheless, challenges remain in predicting structures with weak evolutionary signals, such as nanobody-antigen, antibody-antigen, and viral complexes. Expectedly, modeling large complexes remains also challenging due to their high memory compute demands. In addition to the assembly category, we assessed the accuracy of modeling interdomain interfaces in the tertiary structure prediction targets. Models on seven targets featuring 17 unique interfaces were analyzed. Best predictors achieved the 76.5% success rate, with the UM-TBM group being the leader. In the interdomain category, we observed that the predictors faced challenges, as in the case of the assembly category, when the evolutionary signal for a given domain pair was weak or the structure was large. Overall, CASP15 witnessed unprecedented improvement in interface modeling, reflecting the AI revolution seen in CASP14.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, USA
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
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26
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Nie M, Li H. Innovation in Cross-Linking Mass Spectrometry Workflows: Toward a Comprehensive, Flexible, and Customizable Data Analysis Platform. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1949-1956. [PMID: 37537999 DOI: 10.1021/jasms.3c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is widely used in the analysis of protein structure and protein-protein interactions (PPIs). Throughout the entire workflow, the utilization of cross-linkers and the interpretation of cross-linking data are the core steps. In recent years, the development of cross-linkers and analytical software mostly follow up on the classical models of non-cleavable cross-linkers such as BS3/DSS and MS-cleavable cross-linkers such as DSSO. Although such a paradigm promotes the maturity and robustness of the XL-MS field, it confines the innovation and flexibility of new cross-linkers and analytical software. This critical insight will discuss the classification, advantages, and disadvantages of existing data analysis search engines. Take the new platinum-based metal cross-linker as an example, potential pitfalls in characterization of cross-linked peptides using existing software are discussed. Finally, ideas on developing more flexible, comprehensive, and user-friendly cross-linkers and software tools are proposed.
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Affiliation(s)
- Minhan Nie
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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27
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Burnap SA, Ortega-Prieto AM, Jimenez-Guardeño JM, Ali H, Takov K, Fish M, Shankar-Hari M, Giacca M, Malim MH, Mayr M. Cross-Linking Mass Spectrometry Uncovers Interactions Between High-Density Lipoproteins and the SARS-CoV-2 Spike Glycoprotein. Mol Cell Proteomics 2023; 22:100600. [PMID: 37343697 PMCID: PMC10279469 DOI: 10.1016/j.mcpro.2023.100600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
High-density lipoprotein (HDL) levels are reduced in patients with coronavirus disease 2019 (COVID-19), and the extent of this reduction is associated with poor clinical outcomes. While lipoproteins are known to play a key role during the life cycle of the hepatitis C virus, their influence on coronavirus (CoV) infections is poorly understood. In this study, we utilize cross-linking mass spectrometry (XL-MS) to determine circulating protein interactors of the severe acute respiratory syndrome (SARS)-CoV-2 spike glycoprotein. XL-MS of plasma isolated from patients with COVID-19 uncovered HDL protein interaction networks, dominated by acute-phase serum amyloid proteins, whereby serum amyloid A2 was shown to bind to apolipoprotein (Apo) D. XL-MS on isolated HDL confirmed ApoD to interact with SARS-CoV-2 spike but not SARS-CoV-1 spike. Other direct interactions of SARS-CoV-2 spike upon HDL included ApoA1 and ApoC3. The interaction between ApoD and spike was further validated in cells using immunoprecipitation-MS, which uncovered a novel interaction between both ApoD and spike with membrane-associated progesterone receptor component 1. Mechanistically, XL-MS coupled with data-driven structural modeling determined that ApoD may interact within the receptor-binding domain of the spike. However, ApoD overexpression in multiple cell-based assays had no effect upon viral replication or infectivity. Thus, SARS-CoV-2 spike can bind to apolipoproteins on HDL, but these interactions do not appear to alter infectivity.
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Affiliation(s)
- Sean A Burnap
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK; The Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, UK; King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Jose M Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Hashim Ali
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK; Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Kaloyan Takov
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Matthew Fish
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK; Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Manu Shankar-Hari
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, UK; Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK
| | - Mauro Giacca
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK
| | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Manuel Mayr
- King's College London British Heart Foundation Centre, School of Cardiovascular Medicine and Sciences, London, UK.
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28
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Habeck M. Bayesian methods in integrative structure modeling. Biol Chem 2023; 404:741-754. [PMID: 37505205 DOI: 10.1515/hsz-2023-0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
There is a growing interest in characterizing the structure and dynamics of large biomolecular assemblies and their interactions within the cellular environment. A diverse array of experimental techniques allows us to study biomolecular systems on a variety of length and time scales. These techniques range from imaging with light, X-rays or electrons, to spectroscopic methods, cross-linking mass spectrometry and functional genomics approaches, and are complemented by AI-assisted protein structure prediction methods. A challenge is to integrate all of these data into a model of the system and its functional dynamics. This review focuses on Bayesian approaches to integrative structure modeling. We sketch the principles of Bayesian inference, highlight recent applications to integrative modeling and conclude with a discussion of current challenges and future perspectives.
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Affiliation(s)
- Michael Habeck
- Microscopic Image Analysis Group, Jena University Hospital, D-07743 Jena, Germany
- Max Planck Institute for Multidisciplinary Sciences, d-37077 Göttingen, Germany
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29
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Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD. Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. Anal Chem 2023; 95:10670-10685. [PMID: 37341467 DOI: 10.1021/acs.analchem.3c01369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) is emerging as a method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of cross-linkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable cross-links), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-cross-linkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-cross-linkers have not enjoyed widespread use and are yet to be employed for proteome-wide studies because their products are challenging to identify. Here, we demonstrate the synthesis and application of two heterobifunctional photo-cross-linkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil doubly fissile MS-cleavable linkages upon acyl transfer to protein targets. Moreover, these cross-linkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-cross-linking in cellulo. These studies elucidate a small portion of Escherichia coli's interaction network, albeit with residue-level resolution. With further optimization, these methods will enable the detection of protein quinary interaction networks in their native environment at residue-level resolution, and we expect that they will prove useful toward the effort to explore the molecular sociology of the cell.
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Affiliation(s)
- Anneliese M Faustino
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Piyoosh Sharma
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Edgar Manriquez-Sandoval
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Divya Yadav
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen D Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
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30
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Zhang B, Gao H, Gong Z, Zhao L, Zhong B, Sui Z, Liang Z, Zhang Y, Zhao Q, Zhang L. Improved Cross-Linking Coverage for Protein Complexes Containing Low Levels of Lysine by Using an Enrichable Photo-Cross-Linker. Anal Chem 2023. [PMID: 37303169 DOI: 10.1021/acs.analchem.2c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chemical cross-linking coupled with mass spectrometry (XL-MS) is an important technique for the structural analysis of protein complexes where the coverage of amino acids and the identification of cross-linked sites are crucial. Photo-cross-linking has multisite reactivity and is valuable for the structural analysis of chemical cross-linking. However, a high degree of heterogeneity results from this multisite reactivity, which results in samples with higher complexity and lower abundance. Additionally, the applicability of photo-cross-linking is limited to purified protein complexes. In this work, we demonstrate a photo-cross-linker, alkynyl-succinimidyl-diazirine (ASD) with the reactive groups of N-hydroxysuccinimide ester and diazirine, as well as the click-enrichable alkyne group. Photo-cross-linkers can provide higher site reactivity for proteins that contain only a small number of lysine residues, thereby complementing the more commonly used lysine-targeting cross-linkers. By systematically analyzing proteins with differing lysine contents and differing flexibilities, we demonstrated clear enhancement in structure elucidation for proteins containing less lysine and with high flexibility. In addition, enrichment approaches of alkynyl-azide click chemistry conjugated with biotin-streptavidin purification (coinciding with parallel orthogonal digestion) improved the identification coverage of cross-links. We show that this photo-cross-linking approach can be used for membrane proteome-wide complex analysis. This method led to the identification of a total of 14066 lysine-X cross-linked site pairs from a total of 2784 proteins. Thus, this cross-linker is a valuable addition to a photo-cross-linking toolkit and improves the identification coverage of XL-MS in functional structure analysis.
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Affiliation(s)
- Beirong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zhou Gong
- CAS Innovation Academy for Precision Measurement Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Chinese Academy of Sciences, Wuhan, Hubei 430071, People's Republic of China
| | - Lili Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bowen Zhong
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, People's Republic of China
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31
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Mészáros B, Park E, Malinverni D, Sejdiu BI, Immadisetty K, Sandhu M, Lang B, Babu MM. Recent breakthroughs in computational structural biology harnessing the power of sequences and structures. Curr Opin Struct Biol 2023; 80:102608. [PMID: 37182396 DOI: 10.1016/j.sbi.2023.102608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023]
Abstract
Recent advances in computational approaches and their integration into structural biology enable tackling increasingly complex questions. Here, we discuss several key areas, highlighting breakthroughs and remaining challenges. Theoretical modeling has provided tools to accurately predict and design protein structures on a scale currently difficult to achieve using experimental approaches. Molecular Dynamics simulations have become faster and more precise, delivering actionable information inaccessible by current experimental methods. Virtual screening workflows allow a high-throughput approach to discover ligands that bind and modulate protein function, while Machine Learning methods enable the design of proteins with new functionalities. Integrative structural biology combines several of these approaches, pushing the frontiers of structural and functional characterization to ever larger systems, advancing towards a complete understanding of the living cell. These breakthroughs will accelerate and significantly impact diverse areas of science.
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Affiliation(s)
- Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Electa Park
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Duccio Malinverni
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/DucMalinverni
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/bisejdiu
| | - Kalyan Immadisetty
- Department of Bone Marrow Transplantation & Cellular Therapy, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/k_immadisetty
| | - Manbir Sandhu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/M5andhu
| | - Benjamin Lang
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA. https://twitter.com/langbnj
| | - M Madan Babu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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32
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Wu T, Li ST, Ran Y, Lin Y, Liu L, Zhang X, Zhou L, Zhang L, Wu D, Yang B, Tang S. Mapping protein direct interactome of oxidoreductases with small molecular chemical cross-linkers in live cells. Redox Biol 2023; 61:102642. [PMID: 36863169 PMCID: PMC9986639 DOI: 10.1016/j.redox.2023.102642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Identifying direct substrates of enzymes has been a long-term challenge. Here, we present a strategy using live cell chemical cross-linking and mass spectrometry to identify the putative substrates of enzymes for further biochemical validation. Compared with other methods, our strategy is based on the identification of cross-linked peptides supported by high-quality MS/MS spectra, which eliminates false-positive discoveries of indirect binders. Additionally, cross-linking sites allow the analysis of interaction interfaces, providing further information for substrate validation. We demonstrated this strategy by identifying direct substrates of thioredoxin in both E. coli and HEK293T cells using two bis-vinyl sulfone chemical cross-linkers BVSB and PDES. We confirmed that BVSB and PDES have high specificity in cross-linking the active site of thioredoxin with its substrates both in vitro and in live cells. Applying live cell cross-linking, we identified 212 putative substrates of thioredoxin in E. coli and 299 putative S-nitrosylation (SNO) substrates of thioredoxin in HEK293T cells. In addition to thioredoxin, we have shown that this strategy can be applied to other proteins in the thioredoxin superfamily. Based on these results, we believe future development of cross-linking techniques will further advance cross-linking mass spectrometry in identifying substrates of other classes of enzymes.
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Affiliation(s)
- Ting Wu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Shang-Tong Li
- Glbizzia Biosciences Co., Ltd, Beijing, 102601, China
| | - Yu Ran
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Yinuo Lin
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Lu Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Donghai Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Shibing Tang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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33
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Bartolec TK, Vázquez-Campos X, Norman A, Luong C, Johnson M, Payne RJ, Wilkins MR, Mackay JP, Low JKK. Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein-protein interactions in the human cell. Proc Natl Acad Sci U S A 2023; 120:e2219418120. [PMID: 37071682 PMCID: PMC10151615 DOI: 10.1073/pnas.2219418120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/16/2023] [Indexed: 04/19/2023] Open
Abstract
Significant recent advances in structural biology, particularly in the field of cryoelectron microscopy, have dramatically expanded our ability to create structural models of proteins and protein complexes. However, many proteins remain refractory to these approaches because of their low abundance, low stability, or-in the case of complexes-simply not having yet been analyzed. Here, we demonstrate the power of using cross-linking mass spectrometry (XL-MS) for the high-throughput experimental assessment of the structures of proteins and protein complexes. This included those produced by high-resolution but in vitro experimental data, as well as in silico predictions based on amino acid sequence alone. We present the largest XL-MS dataset to date, describing 28,910 unique residue pairs captured across 4,084 unique human proteins and 2,110 unique protein-protein interactions. We show that models of proteins and their complexes predicted by AlphaFold2, and inspired and corroborated by the XL-MS data, offer opportunities to deeply mine the structural proteome and interactome and reveal mechanisms underlying protein structure and function.
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Affiliation(s)
- Tara K. Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Xabier Vázquez-Campos
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Alexander Norman
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
| | - Clement Luong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Marcus Johnson
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Richard J. Payne
- School of Chemistry, University of Sydney, Sydney, NSW2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW2006, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Randwick, NSW2052, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW2006, Australia
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34
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Chen ZA, Rappsilber J. Protein structure dynamics by crosslinking mass spectrometry. Curr Opin Struct Biol 2023; 80:102599. [PMID: 37104977 DOI: 10.1016/j.sbi.2023.102599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Crosslinking mass spectrometry captures protein structures in solution. The crosslinks reveal spatial proximities as distance restraints, but do not easily reveal which of these restraints derive from the same protein conformation. This superposition can be reduced by photo-crosslinking, and adding information from protein structure models, or quantitative crosslinking reveals conformation-specific crosslinks. As a consequence, crosslinking MS has proven useful already in the context of multiple dynamic protein systems. We foresee a breakthrough in the resolution and scale of studying protein dynamics when crosslinks are used to guide deep-learning-based protein modelling. Advances in crosslinking MS, such as photoactivatable crosslinking and in-situ crosslinking, will then reveal protein conformation dynamics in the cellular context, at a pseudo-atomic resolution, and plausibly in a time-resolved manner.
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Affiliation(s)
- Zhuo Angel Chen
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany
| | - Juri Rappsilber
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany; Si-M/"Der Simulierte Mensch", a Science Framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, 10623 Berlin, Germany; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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35
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Zamel J, Chen J, Zaer S, Harris PD, Drori P, Lebendiker M, Kalisman N, Dokholyan NV, Lerner E. Structural and dynamic insights into α-synuclein dimer conformations. Structure 2023; 31:411-423.e6. [PMID: 36809765 PMCID: PMC10081966 DOI: 10.1016/j.str.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/22/2023]
Abstract
Parkinson disease is associated with the aggregation of the protein α-synuclein. While α-synuclein can exist in multiple oligomeric states, the dimer has been a subject of extensive debates. Here, using an array of biophysical approaches, we demonstrate that α-synuclein in vitro exhibits primarily a monomer-dimer equilibrium in nanomolar concentrations and up to a few micromolars. We then use spatial information from hetero-isotopic cross-linking mass spectrometry experiments as restrains in discrete molecular dynamics simulations to obtain the ensemble structure of dimeric species. Out of eight structural sub-populations of dimers, we identify one that is compact, stable, abundant, and exhibits partially exposed β-sheet structures. This compact dimer is the only one where the hydroxyls of tyrosine 39 are in proximity that may promote dityrosine covalent linkage upon hydroxyl radicalization, which is implicated in α-synuclein amyloid fibrils. We propose that this α-synuclein dimer features etiological relevance to Parkinson disease.
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Affiliation(s)
- Joanna Zamel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Jiaxing Chen
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Sofia Zaer
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Paz Drori
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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36
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Lee K, O'Reilly FJ. Cross-linking mass spectrometry for mapping protein complex topologies in situ. Essays Biochem 2023; 67:215-228. [PMID: 36734207 PMCID: PMC10070479 DOI: 10.1042/ebc20220168] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/04/2023]
Abstract
Cross-linking mass spectrometry has become an established technology to provide structural information on the topology and dynamics of protein complexes. Readily accessible workflows can provide detailed data on simplified systems, such as purified complexes. However, using this technology to study the structure of protein complexes in situ, such as in organelles, cells, and even tissues, is still a technological frontier. The complexity of these systems remains a considerable challenge, but there have been dramatic improvements in sample handling, data acquisition, and data processing. Here, we summarise these developments and describe the paths towards comprehensive and comparative structural interactomes by cross-linking mass spectrometry.
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Affiliation(s)
- Kitaik Lee
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD 21702-1201, U.S.A
| | - Francis J O'Reilly
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute (NCI), Frederick, MD 21702-1201, U.S.A
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37
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Britt HM, Beveridge R, Calabrese AN. A special issue of Essays in Biochemistry on structural mass spectrometry. Essays Biochem 2023; 67:147-149. [PMID: 36988080 PMCID: PMC10070473 DOI: 10.1042/ebc20230006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 03/30/2023]
Abstract
Mass spectrometry (MS) is now established as an analytical tool to interrogate the structure and dynamics of proteins and their assemblies. An array of MS-based technologies has been developed, with each providing unique information pertaining to protein structure, and forming the heart of integrative structural biology studies. This special issue includes a collection of review articles that discuss both established and emerging structural MS methodologies, along with examples of how these technologies are being deployed to interrogate protein structure and function. Combined, this collection highlights the immense potential of the structural MS toolkit in the study of molecular mechanisms underpinning cellular homeostasis and disease.
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Affiliation(s)
- Hannah M Britt
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K
- The Kavli Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, U.K
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, U.K
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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38
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Shu X, Liao QQ, Li ST, Liu L, Zhang X, Zhou L, Zhang L, Coin I, Wang L, Wu H, Yang B. Detecting Active Deconjugating Enzymes with Genetically Encoded Activity-Based Ubiquitin and Ubiquitin-like Protein Probes. Anal Chem 2023; 95:846-853. [PMID: 36595388 DOI: 10.1021/acs.analchem.2c03270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Post-translational modification of proteins by Ubiquitin (Ub) and Ubiquitin-like proteins (Ubls) can be reversed by deconjugating enzymes, which have been implicated in different pathways and associated with various human diseases. To understand the activity and dynamics of deconjugating enzymes, multiple synthetic and semi-synthetic Ub/Ubl probes have been developed, and some of them have been applied to screen inhibitors of deconjugating enzymes. Since these Ub/Ubl probes are generally not cell-permeable, different strategies have been developed to deliver Ub/Ubl probes to live cells. However, till now, no Ub/Ubl probes can be expressed in live cells to directly report on the activities of deconjugating enzymes in the most relevant cellular environment. Here, we genetically encoded cross-linkable Ub/Ubl probes in live E. coli and HEK293T cells. These probes can cross-link with deconjugating enzymes in vitro and in vivo. Using these Ub probes combined with mass spectrometry, we have successfully identified endogenous deconjugating enzymes in live cells. We believe that these genetically encoded Ub/Ubl probes are valuable for investigating biological functions of deconjugating enzymes in physiological environments.
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Affiliation(s)
- Xin Shu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing-Qing Liao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shang-Tong Li
- Glbizzia Biosciences Company Limited, Beijing 102601, China
| | - Lu Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Long Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig 04103, Germany
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Haifan Wu
- Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China
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39
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Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable AL, Fang T, Doncheva N, Pyysalo S, Bork P, Jensen L, von Mering C. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res 2023; 51:D638-D646. [PMID: 36370105 PMCID: PMC9825434 DOI: 10.1093/nar/gkac1000] [Citation(s) in RCA: 1530] [Impact Index Per Article: 1530.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
Much of the complexity within cells arises from functional and regulatory interactions among proteins. The core of these interactions is increasingly known, but novel interactions continue to be discovered, and the information remains scattered across different database resources, experimental modalities and levels of mechanistic detail. The STRING database (https://string-db.org/) systematically collects and integrates protein-protein interactions-both physical interactions as well as functional associations. The data originate from a number of sources: automated text mining of the scientific literature, computational interaction predictions from co-expression, conserved genomic context, databases of interaction experiments and known complexes/pathways from curated sources. All of these interactions are critically assessed, scored, and subsequently automatically transferred to less well-studied organisms using hierarchical orthology information. The data can be accessed via the website, but also programmatically and via bulk downloads. The most recent developments in STRING (version 12.0) are: (i) it is now possible to create, browse and analyze a full interaction network for any novel genome of interest, by submitting its complement of encoded proteins, (ii) the co-expression channel now uses variational auto-encoders to predict interactions, and it covers two new sources, single-cell RNA-seq and experimental proteomics data and (iii) the confidence in each experimentally derived interaction is now estimated based on the detection method used, and communicated to the user in the web-interface. Furthermore, STRING continues to enhance its facilities for functional enrichment analysis, which are now fully available also for user-submitted genomes.
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Affiliation(s)
- Damian Szklarczyk
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Rebecca Kirsch
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Mikaela Koutrouli
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Katerina Nastou
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Farrokh Mehryary
- TurkuNLP lab, Department of Computing, University of Turku, 20014 Turku, Finland
| | - Radja Hachilif
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Annika L Gable
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tao Fang
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sampo Pyysalo
- TurkuNLP lab, Department of Computing, University of Turku, 20014 Turku, Finland
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul 03722, South Korea
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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40
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Le Sueur C, Hammarén HM, Sridharan S, Savitski MM. Thermal proteome profiling: Insights into protein modifications, associations, and functions. Curr Opin Chem Biol 2022; 71:102225. [PMID: 36368297 DOI: 10.1016/j.cbpa.2022.102225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022]
Abstract
Tracking proteins' biophysical characteristics on a proteome-wide scale can provide valuable information on their functions and interactions. Thermal proteome profiling (TPP) is a multiplexed quantitative proteomics approach that measures changes in protein thermal stability-a key biophysical property-across different cellular states. Developed in 2014, as a target-deconvolution assay for drugs and other small molecules, TPP has since evolved to a system-level biochemical omics technique providing insights into context-dependent changes in protein states. In this review, we summarise key advances in the experimental and data analysis pipeline that have aided this transformation and discuss the recent developments and applications of TPP.
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Affiliation(s)
- Cecile Le Sueur
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Henrik M Hammarén
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Barts Brain Tumour Center, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
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41
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New opportunities in integrative structural modeling. Curr Opin Struct Biol 2022; 77:102488. [PMID: 36279817 DOI: 10.1016/j.sbi.2022.102488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]
Abstract
Integrative structural modeling enables structure determination of macromolecules and their complexes by integrating data from multiple sources. It has been successfully used to characterize macromolecular structures when a single structural biology technique was insufficient. Recent developments in cellular structural biology, including in-cell cryo-electron tomography and artificial intelligence-based structure prediction, have created new opportunities for integrative structural modeling. Here, we will review these opportunities along with the latest developments in integrative modeling methods and their applications. We also highlight open challenges and directions for further development.
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42
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Pierro A, Bonucci A, Normanno D, Ansaldi M, Pilet E, Ouari O, Guigliarelli B, Etienne E, Gerbaud G, Magalon A, Belle V, Mileo E. Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide‐Based EPR Spectroscopy. Chemistry 2022; 28:e202202249. [DOI: 10.1002/chem.202202249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Annalisa Pierro
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
- Department of Chemistry University of Konstanz, and Konstanz Research School Chemical Biology 78457 Konstanz Germany
| | - Alessio Bonucci
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Davide Normanno
- Aix Marseille Univ CNRS, Inserm Institut Paoli-Calmettes, CRCM Centre de Recherche en Cancérologie de Marseille 13273 Marseille France
- Univ Montpellier CNRS, IGH Institut de Génétique Humaine 34396 Montpellier France
| | - Mireille Ansaldi
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Eric Pilet
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Olivier Ouari
- Aix Marseille Univ CNRS, ICR Institut de Chimie Radicalaire 13397 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Emilien Etienne
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Guillaume Gerbaud
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Axel Magalon
- Aix Marseille Univ CNRS, LCB Laboratoire de Chimie Bacterienne, IMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille Univ CNRS, BIP Bioénérgetique et Ingénierie des Protéines, IMM 13009 Marseille France
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43
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Lorentzen J, Pedersen DV, Gadeberg TAF, Andersen GR. Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging. Protein Sci 2022; 31:e4432. [PMID: 36173177 PMCID: PMC9601772 DOI: 10.1002/pro.4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022]
Abstract
Structure determination of macromolecular complexes is challenging if subunits can dissociate during crystallization or preparation of electron microscopy grids. We present an approach where a labile complex is stabilized by linking subunits though introduction of a peptide tag in one subunit that is recognized by a nanobody tethered to a second subunit. This allowed crystal structure determination at 3.9 Å resolution of the highly non‐globular 320 kDa proconvertase formed by complement components C3b, factor B, and properdin. Whereas the binding mode of properdin to C3b is preserved, an internal rearrangement occurs in the zymogen factor B von Willebrand domain type A domain compared to the proconvertase not bound to properdin. The structure emphasizes the role of two noncanonical loops in thrombospondin repeats 5 and 6 of properdin in augmenting the activity of the C3 convertase. We suggest that linking of subunits through peptide specific tethered nanobodies represents a simple alternative to approaches like affinity maturation and chemical cross‐linking for the stabilization of large macromolecular complexes. Besides applications for structural biology, nanobody bridging may become a new tool for biochemical analysis of unstable macromolecular complexes and in vitro selection of highly specific binders for such complexes. PDB Code(s): 7NOZ;
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Affiliation(s)
- Josefine Lorentzen
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
| | | | - Trine Amalie Fogh Gadeberg
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
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44
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The augmin complex architecture reveals structural insights into microtubule branching. Nat Commun 2022; 13:5635. [PMID: 36163468 PMCID: PMC9512787 DOI: 10.1038/s41467-022-33228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
In mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our understanding of augmin-mediated microtubule branching is hampered by the lack of structural information on the augmin complex. Here, we elucidate the molecular architecture and conformational plasticity of the augmin complex using an integrative structural biology approach. The elongated structure of the augmin complex is characterised by extensive coiled-coil segments and comprises two structural elements with distinct but complementary functions in γ-TuRC and microtubule binding, linked by a flexible hinge. The augmin complex is recruited to microtubules via a composite microtubule binding site comprising a positively charged unordered extension and two calponin homology domains. Our study provides the structural basis for augmin function in branched microtubule formation, decisively fostering our understanding of spindle formation in mitosis. The formation of branched microtubule networks in mitotic spindles depends on the augmin complex. Zupa, Würtz et al. elucidate the molecular architecture and conformational plasticity of the augmin complex using integrative structural biology, providing structural insights into microtubule branching.
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45
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Gabel CA, Li Z, DeMarco AG, Zhang Z, Yang J, Hall MC, Barford D, Chang L. Molecular architecture of the augmin complex. Nat Commun 2022; 13:5449. [PMID: 36114186 PMCID: PMC9481612 DOI: 10.1038/s41467-022-33227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 09/05/2022] [Indexed: 12/21/2022] Open
Abstract
Accurate segregation of chromosomes during mitosis depends on the correct assembly of the mitotic spindle, a bipolar structure composed mainly of microtubules. The augmin complex, or homologous to augmin subunits (HAUS) complex, is an eight-subunit protein complex required for building robust mitotic spindles in metazoa. Augmin increases microtubule density within the spindle by recruiting the γ-tubulin ring complex (γ-TuRC) to pre-existing microtubules and nucleating branching microtubules. Here, we elucidate the molecular architecture of augmin by single particle cryo-electron microscopy (cryo-EM), computational methods, and crosslinking mass spectrometry (CLMS). Augmin's highly flexible structure contains a V-shaped head and a filamentous tail, with the head existing in either extended or contracted conformational states. Our work highlights how cryo-EM, complemented by computational advances and CLMS, can elucidate the structure of a challenging protein complex and provides insights into the function of augmin in mediating microtubule branching nucleation.
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Affiliation(s)
- Clinton A Gabel
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Andrew G DeMarco
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Mark C Hall
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022; 30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.
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Affiliation(s)
- Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland; Systems Biology PhD Program, University of Zürich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland.
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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules 2022; 27:1841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein-protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein-protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein-protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein-protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
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